Differential Exp Analysis for TMA36 (extreme groups)
Mafe Senosain
2020-02-18
Using Random Forest classification
Endothelial cells
## Using CANARY as id variables
## Confusion Matrix and Statistics
##
## Reference
## Prediction G P
## G 226 143
## P 153 1031
##
## Accuracy : 0.8094
## 95% CI : (0.789, 0.8287)
## No Information Rate : 0.756
## P-Value [Acc > NIR] : 2.813e-07
##
## Kappa : 0.4788
##
## Mcnemar's Test P-Value : 0.6009
##
## Sensitivity : 0.5963
## Specificity : 0.8782
## Pos Pred Value : 0.6125
## Neg Pred Value : 0.8708
## Precision : 0.6125
## Recall : 0.5963
## F1 : 0.6043
## Prevalence : 0.2440
## Detection Rate : 0.1455
## Detection Prevalence : 0.2376
## Balanced Accuracy : 0.7373
##
## 'Positive' Class : G
## Fibroblasts and Mesenchymal cells
## Using CANARY as id variables
## Confusion Matrix and Statistics
##
## Reference
## Prediction G P
## G 634 243
## P 366 6787
##
## Accuracy : 0.9242
## 95% CI : (0.9182, 0.9299)
## No Information Rate : 0.8755
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.6328
##
## Mcnemar's Test P-Value : 7.666e-07
##
## Sensitivity : 0.63400
## Specificity : 0.96543
## Pos Pred Value : 0.72292
## Neg Pred Value : 0.94883
## Precision : 0.72292
## Recall : 0.63400
## F1 : 0.67555
## Prevalence : 0.12453
## Detection Rate : 0.07895
## Detection Prevalence : 0.10922
## Balanced Accuracy : 0.79972
##
## 'Positive' Class : G
## T cells
## Using CANARY as id variables
## Confusion Matrix and Statistics
##
## Reference
## Prediction G P
## G 1359 1324
## P 797 15672
##
## Accuracy : 0.8893
## 95% CI : (0.8847, 0.8937)
## No Information Rate : 0.8874
## P-Value [Acc > NIR] : 0.2155
##
## Kappa : 0.4992
##
## Mcnemar's Test P-Value : <2e-16
##
## Sensitivity : 0.63033
## Specificity : 0.92210
## Pos Pred Value : 0.50652
## Neg Pred Value : 0.95161
## Precision : 0.50652
## Recall : 0.63033
## F1 : 0.56169
## Prevalence : 0.11257
## Detection Rate : 0.07096
## Detection Prevalence : 0.14009
## Balanced Accuracy : 0.77622
##
## 'Positive' Class : G
## CD8+ T cells
## Using CANARY as id variables
## Confusion Matrix and Statistics
##
## Reference
## Prediction G P
## G 526 284
## P 205 3841
##
## Accuracy : 0.8993
## 95% CI : (0.8905, 0.9076)
## No Information Rate : 0.8495
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.623
##
## Mcnemar's Test P-Value : 0.0004198
##
## Sensitivity : 0.7196
## Specificity : 0.9312
## Pos Pred Value : 0.6494
## Neg Pred Value : 0.9493
## Precision : 0.6494
## Recall : 0.7196
## F1 : 0.6827
## Prevalence : 0.1505
## Detection Rate : 0.1083
## Detection Prevalence : 0.1668
## Balanced Accuracy : 0.8254
##
## 'Positive' Class : G
## CD4+ T cells
## Using CANARY as id variables
## Confusion Matrix and Statistics
##
## Reference
## Prediction G P
## G 453 516
## P 198 5943
##
## Accuracy : 0.8996
## 95% CI : (0.8924, 0.9065)
## No Information Rate : 0.9084
## P-Value [Acc > NIR] : 0.9951
##
## Kappa : 0.505
##
## Mcnemar's Test P-Value : <2e-16
##
## Sensitivity : 0.69585
## Specificity : 0.92011
## Pos Pred Value : 0.46749
## Neg Pred Value : 0.96776
## Precision : 0.46749
## Recall : 0.69585
## F1 : 0.55926
## Prevalence : 0.09156
## Detection Rate : 0.06371
## Detection Prevalence : 0.13629
## Balanced Accuracy : 0.80798
##
## 'Positive' Class : G
## Myeloid cells
## Using CANARY as id variables
## Confusion Matrix and Statistics
##
## Reference
## Prediction G P
## G 783 301
## P 214 5597
##
## Accuracy : 0.9253
## 95% CI : (0.9188, 0.9314)
## No Information Rate : 0.8554
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.7086
##
## Mcnemar's Test P-Value : 0.0001509
##
## Sensitivity : 0.7854
## Specificity : 0.9490
## Pos Pred Value : 0.7223
## Neg Pred Value : 0.9632
## Precision : 0.7223
## Recall : 0.7854
## F1 : 0.7525
## Prevalence : 0.1446
## Detection Rate : 0.1136
## Detection Prevalence : 0.1572
## Balanced Accuracy : 0.8672
##
## 'Positive' Class : G
## NK cells
## Using CANARY as id variables
## Confusion Matrix and Statistics
##
## Reference
## Prediction G P
## G 344 52
## P 65 814
##
## Accuracy : 0.9082
## 95% CI : (0.891, 0.9235)
## No Information Rate : 0.6792
## P-Value [Acc > NIR] : <2e-16
##
## Kappa : 0.7876
##
## Mcnemar's Test P-Value : 0.2673
##
## Sensitivity : 0.8411
## Specificity : 0.9400
## Pos Pred Value : 0.8687
## Neg Pred Value : 0.9261
## Precision : 0.8687
## Recall : 0.8411
## F1 : 0.8547
## Prevalence : 0.3208
## Detection Rate : 0.2698
## Detection Prevalence : 0.3106
## Balanced Accuracy : 0.8905
##
## 'Positive' Class : G
## Epithelial cells
## Using CANARY as id variables
## Confusion Matrix and Statistics
##
## Reference
## Prediction G P
## G 1766 687
## P 710 15185
##
## Accuracy : 0.9239
## 95% CI : (0.9199, 0.9277)
## No Information Rate : 0.8651
## P-Value [Acc > NIR] : <2e-16
##
## Kappa : 0.6726
##
## Mcnemar's Test P-Value : 0.5561
##
## Sensitivity : 0.71325
## Specificity : 0.95672
## Pos Pred Value : 0.71993
## Neg Pred Value : 0.95533
## Precision : 0.71993
## Recall : 0.71325
## F1 : 0.71658
## Prevalence : 0.13495
## Detection Rate : 0.09625
## Detection Prevalence : 0.13369
## Balanced Accuracy : 0.83498
##
## 'Positive' Class : G
## Comparing Median expression of each marker per cell type
Endothelial cells
## Using CANARY, pt_ID as id variables
## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.47070551 0.5824502
## 2 142Nd_ccasp3 0.95892310 0.9589231
## 3 144Nd_HLA-ABC 0.17614084 0.5724070
## 4 145Nd_CD31 0.32258717 0.5824502
## 5 146Nd_Thioredoxin 0.23168319 0.5724070
## 6 147Sm_b-CAT 0.74318872 0.7823039
## 7 151Eu_TTF1 0.35278528 0.5824502
## 8 153Eu_Ki67 0.25608663 0.5724070
## 9 154Sm_CD45 0.22168819 0.5724070
## 10 156Gd_Vimentin 0.27468896 0.5724070
## 11 158Gd_p-STAT3 0.47913331 0.5824502
## 12 159Tb_CD4 0.18101154 0.5724070
## 13 160Gd_MDM2 0.49508264 0.5824502
## 14 161Dy_Cytokeratin 0.28620351 0.5724070
## 15 162Dy_MET 0.44735653 0.5824502
## 16 163Dy_TP63 0.02102468 0.4204935
## 17 164Dy_CK7 0.09186981 0.5724070
## 18 165Ho_EGFR 0.37935787 0.5824502
## 19 174Yb_HLA-DR 0.11165386 0.5724070
## 20 175Lu_PD-L1 0.67040646 0.7448961Fibroblasts/Mesenchymal cells
## Using CANARY, pt_ID as id variables
## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.251800611 0.4333774
## 2 142Nd_ccasp3 0.606497326 0.7412745
## 3 144Nd_HLA-ABC 0.917901965 0.9197583
## 4 145Nd_CD31 0.718163959 0.7899804
## 5 147Sm_b-CAT 0.216247330 0.4333774
## 6 151Eu_TTF1 0.359097978 0.5266770
## 7 153Eu_Ki67 0.256086630 0.4333774
## 8 154Sm_CD45 0.511298970 0.6616810
## 9 155Gd_CD56 0.919758300 0.9197583
## 10 156Gd_Vimentin 0.052045561 0.3278738
## 11 158Gd_p-STAT3 0.511298970 0.6616810
## 12 159Tb_CD4 0.100989632 0.3278738
## 13 160Gd_MDM2 0.119226847 0.3278738
## 14 161Dy_Cytokeratin 0.286203511 0.4497484
## 15 162Dy_MET 0.230376074 0.4333774
## 16 163Dy_TP63 0.094703337 0.3278738
## 17 164Dy_CK7 0.038040141 0.3278738
## 18 165Ho_EGFR 0.114680175 0.3278738
## 19 166Er_CD44 0.101930635 0.3278738
## 20 170Yb_CD3 0.699267261 0.7899804
## 21 172Yb_p-S6 0.135245907 0.3306011
## 22 174Yb_HLA-DR 0.007813437 0.1718956Immune cells
## Using CANARY, pt_ID as id variables
## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.30270519 0.5900982
## 2 144Nd_HLA-ABC 0.17815278 0.5302752
## 3 145Nd_CD31 0.12074819 0.4469706
## 4 151Eu_TTF1 0.73699603 0.8206337
## 5 153Eu_Ki67 0.42322718 0.5900982
## 6 154Sm_CD45 0.12415850 0.4469706
## 7 156Gd_Vimentin 0.01538856 0.2769940
## 8 158Gd_p-STAT3 0.20691654 0.5302752
## 9 159Tb_CD4 0.23567786 0.5302752
## 10 160Gd_MDM2 0.47084087 0.6053668
## 11 162Dy_MET 0.42273745 0.5900982
## 12 163Dy_TP63 0.82063372 0.8206337
## 13 164Dy_CK7 0.51005544 0.6120665
## 14 165Ho_EGFR 0.42618206 0.5900982
## 15 166Er_CD44 0.41810901 0.5900982
## 16 170Yb_CD3 0.82063372 0.8206337
## 17 171Yb_CD11b 0.04341486 0.3907337
## 18 174Yb_HLA-DR 0.08454391 0.4469706T cells
## Using CANARY, pt_ID as id variables
## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.69584622 0.6958462
## 2 144Nd_HLA-ABC 0.05834773 0.3306371
## 3 145Nd_CD31 0.21259674 0.6004439
## 4 151Eu_TTF1 0.60262668 0.6402908
## 5 153Eu_Ki67 0.28256182 0.6004439
## 6 154Sm_CD45 0.04003110 0.3306371
## 7 156Gd_Vimentin 0.03035444 0.3306371
## 8 159Tb_CD4 0.42451245 0.6013926
## 9 160Gd_MDM2 0.58862222 0.6402908
## 10 162Dy_MET 0.40662831 0.6013926
## 11 163Dy_TP63 0.51129897 0.6402908
## 12 164Dy_CK7 0.08097799 0.3404075
## 13 165Ho_EGFR 0.58304927 0.6402908
## 14 166Er_CD44 0.10011984 0.3404075
## 15 168Er_CD8 0.38117376 0.6013926
## 16 170Yb_CD3 0.34837291 0.6013926
## 17 174Yb_HLA-DR 0.26763702 0.6004439CD8 T cells
## Using CANARY, pt_ID as id variables
## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.779100821 0.9364463
## 2 144Nd_HLA-ABC 0.004201291 0.1092336
## 3 145Nd_CD31 0.864411934 0.9364463
## 4 148Nd_HER2 0.064621030 0.3561469
## 5 150Nd_p-STAT5 0.937076506 0.9685137
## 6 151Eu_TTF1 0.798329996 0.9364463
## 7 153Eu_Ki67 0.348881570 0.8246292
## 8 154Sm_CD45 0.055597903 0.3561469
## 9 155Gd_CD56 0.085240901 0.3561469
## 10 156Gd_Vimentin 0.095885706 0.3561469
## 11 159Tb_CD4 0.394032207 0.8537364
## 12 160Gd_MDM2 0.847177570 0.9364463
## 13 161Dy_Cytokeratin 0.968513746 0.9685137
## 14 162Dy_MET 0.443515326 0.8870307
## 15 163Dy_TP63 0.198039328 0.5731536
## 16 164Dy_CK7 0.081171972 0.3561469
## 17 165Ho_EGFR 0.691734433 0.9364463
## 18 166Er_CD44 0.217233300 0.5731536
## 19 167Er_p-ERK 0.782667731 0.9364463
## 20 168Er_CD8 0.597706027 0.9364463
## 21 169Tm_CD24 0.076069146 0.3561469
## 22 170Yb_CD3 0.478294283 0.8882608
## 23 171Yb_CD11b 0.683747538 0.9364463
## 24 172Yb_p-S6 0.664654705 0.9364463
## 25 174Yb_HLA-DR 0.536993609 0.9307889
## 26 175Lu_PD-L1 0.220443712 0.5731536CD4 T cells
## Using CANARY, pt_ID as id variables
## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.875266433 0.9336175
## 2 144Nd_HLA-ABC 0.088468197 0.2830982
## 3 151Eu_TTF1 0.533691210 0.7115883
## 4 153Eu_Ki67 0.307529890 0.4920478
## 5 154Sm_CD45 0.084543911 0.2830982
## 6 156Gd_Vimentin 0.007139752 0.1142360
## 7 159Tb_CD4 0.361721725 0.5261407
## 8 160Gd_MDM2 0.801083915 0.9155245
## 9 161Dy_Cytokeratin 0.979433173 0.9794332
## 10 162Dy_MET 0.229653274 0.4490272
## 11 163Dy_TP63 0.231683186 0.4490272
## 12 164Dy_CK7 0.126909027 0.3384241
## 13 165Ho_EGFR 0.656256661 0.8077005
## 14 166Er_CD44 0.042801717 0.2830982
## 15 170Yb_CD3 0.252577790 0.4490272
## 16 174Yb_HLA-DR 0.084434343 0.2830982Myeloid cells
## Using CANARY, pt_ID as id variables
## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.519696825 0.73368963
## 2 144Nd_HLA-ABC 0.327013456 0.62751609
## 3 145Nd_CD31 0.877203626 0.93891013
## 4 146Nd_Thioredoxin 0.958908228 0.95890823
## 5 147Sm_b-CAT 0.302196788 0.62751609
## 6 151Eu_TTF1 0.502686766 0.73368963
## 7 153Eu_Ki67 0.339904550 0.62751609
## 8 154Sm_CD45 0.084543911 0.35594601
## 9 155Gd_CD56 0.335327658 0.62751609
## 10 156Gd_Vimentin 0.084543911 0.35594601
## 11 158Gd_p-STAT3 0.801083915 0.93891013
## 12 159Tb_CD4 0.003921026 0.09376124
## 13 160Gd_MDM2 0.152242116 0.45672635
## 14 161Dy_Cytokeratin 0.241979190 0.62751609
## 15 162Dy_MET 0.088986503 0.35594601
## 16 163Dy_TP63 0.463456332 0.73368963
## 17 164Dy_CK7 0.125389877 0.42990815
## 18 165Ho_EGFR 0.072586747 0.35594601
## 19 166Er_CD44 0.899788877 0.93891013
## 20 170Yb_CD3 0.596163603 0.77538141
## 21 171Yb_CD11b 0.403568549 0.69183180
## 22 172Yb_p-S6 0.613843615 0.77538141
## 23 174Yb_HLA-DR 0.007813437 0.09376124
## 24 175Lu_PD-L1 0.840290669 0.93891013NK cells
## Using CANARY, pt_ID as id variables
## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.743188717 0.8617875
## 2 142Nd_ccasp3 0.762350452 0.8617875
## 3 144Nd_HLA-ABC 0.062807797 0.3266005
## 4 145Nd_CD31 0.448056957 0.8448014
## 5 146Nd_Thioredoxin 0.246484993 0.8448014
## 6 147Sm_b-CAT 0.416946389 0.8448014
## 7 148Nd_HER2 0.011611172 0.1509452
## 8 150Nd_p-STAT5 0.649847205 0.8448014
## 9 151Eu_TTF1 0.535889780 0.8448014
## 10 152Sm_p-AKT 0.527776242 0.8448014
## 11 153Eu_Ki67 0.360292858 0.8448014
## 12 154Sm_CD45 0.089513314 0.3878910
## 13 155Gd_CD56 1.000000000 1.0000000
## 14 156Gd_Vimentin 0.021024677 0.1822139
## 15 158Gd_p-STAT3 0.495082636 0.8448014
## 16 159Tb_CD4 1.000000000 1.0000000
## 17 160Gd_MDM2 0.631740961 0.8448014
## 18 161Dy_Cytokeratin 0.879879917 0.9532032
## 19 162Dy_MET 0.486698306 0.8448014
## 20 163Dy_TP63 0.561488287 0.8448014
## 21 164Dy_CK7 0.757285150 0.8617875
## 22 165Ho_EGFR 0.350524782 0.8448014
## 23 166Er_CD44 0.613843615 0.8448014
## 24 172Yb_p-S6 0.028599489 0.1858967
## 25 174Yb_HLA-DR 0.004459218 0.1159397
## 26 175Lu_PD-L1 0.439747569 0.8448014Epithelial cells
## Using CANARY, pt_ID as id variables
## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.25716783 0.5071181
## 2 142Nd_ccasp3 0.21199182 0.5071181
## 3 144Nd_HLA-ABC 0.30144693 0.5167662
## 4 145Nd_CD31 0.21449027 0.5071181
## 5 146Nd_Thioredoxin 0.91795032 0.9197583
## 6 147Sm_b-CAT 0.14213323 0.5071181
## 7 148Nd_HER2 0.03492253 0.2793803
## 8 150Nd_p-STAT5 0.52777624 0.7037017
## 9 151Eu_TTF1 0.68025814 0.8163098
## 10 153Eu_Ki67 0.12805732 0.5071181
## 11 154Sm_CD45 0.17614084 0.5071181
## 12 155Gd_CD56 0.02343785 0.2793803
## 13 156Gd_Vimentin 0.38932196 0.6229151
## 14 158Gd_p-STAT3 0.80108392 0.8739097
## 15 159Tb_CD4 0.23533821 0.5071181
## 16 160Gd_MDM2 0.25257779 0.5071181
## 17 161Dy_Cytokeratin 0.02267177 0.2793803
## 18 162Dy_MET 0.41810901 0.6271635
## 19 163Dy_TP63 0.78165245 0.8739097
## 20 164Dy_CK7 0.27468896 0.5071181
## 21 165Ho_EGFR 0.62440628 0.7887237
## 22 170Yb_CD3 0.91975830 0.9197583
## 23 174Yb_HLA-DR 0.10471596 0.5071181
## 24 175Lu_PD-L1 0.50268677 0.7037017